Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008513.1 Kokia drynarioides strain JFW-HI SEQ_123189, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 5231
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.25
Found at i:4172 original size:18 final size:18
Alignment explanation
Indices: 4149--4184 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
4139 GCATCTAACA
*
4149 TTGTTCCTTGTAATTATT
1 TTGTTCCTTGTAAATATT
4167 TTGTTCCTTGTAAATATT
1 TTGTTCCTTGTAAATATT
4185 CGGTAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.11, G:0.11, T:0.58
Consensus pattern (18 bp):
TTGTTCCTTGTAAATATT
Found at i:4678 original size:49 final size:49
Alignment explanation
Indices: 4610--4847 Score: 243
Period size: 49 Copynumber: 4.9 Consensus size: 49
4600 GTACCGCGAA
*
4610 ACATGAAGGGAAAGATTTAAGCCGTAACGGCGAATCCAGTACCATGAAG
1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCATGAAG
* * * * *
4659 ACATGGAGGTAAAGGTTTAAGTCGCAACGACGAA-CCATGTACC-TCAGAAG
1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCA-GTACCAT--GAAG
* * * *
4709 ACACGAAGGGAAAGATTTAAGCCGCAGCAGCGAATCC-GATACCA-CAGAG
1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAG-TACCATGA-AG
* * * * *
4758 ACATAAAGGGAAATATTTAGGCCGCAATGGCGAATCCAGTACCACGAAG
1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCATGAAG
* *
4807 ACACGAAGGG-AAGATTTAAGCCGCAATGGCGAATCCAGTAC
1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTAC
4848 ATAGCAACAG
Statistics
Matches: 153, Mismatches: 27, Indels: 19
0.77 0.14 0.10
Matches are distributed among these distances:
48 34 0.22
49 81 0.53
50 36 0.24
51 2 0.01
ACGTcount: A:0.38, C:0.21, G:0.26, T:0.15
Consensus pattern (49 bp):
ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCATGAAG
Found at i:4800 original size:99 final size:98
Alignment explanation
Indices: 4600--4847 Score: 263
Period size: 99 Copynumber: 2.5 Consensus size: 98
4590 ATAGGTCTTA
* * * * * *
4600 GTACCGCGAA-ACATGAAGGGAAAGATTTAAGCCGTAACGGCGAATCCAGTACCATGAAGACATG
1 GTACCACGAAGACACGAAGGGAAAGATTTAAGCCGCAACAGCGAATCCAGTACCAAGAAGACATA
* * * *
4664 GAGGTAAAGGTTTAAGTCGCAACGACGAACCAT
66 AAGGGAAAGATTTAAGCCGCAACGACGAACCAT
* *
4697 GTACCTCAGAAGACACGAAGGGAAAGATTTAAGCCGCAGCAGCGAATCC-GATACCACAG-AGAC
1 GTACCAC-GAAGACACGAAGGGAAAGATTTAAGCCGCAACAGCGAATCCAG-TACCA-AGAAGAC
* * * *
4760 ATAAAGGGAAATATTTAGGCCGCAATGGCGAATCCA-
63 ATAAAGGGAAAGATTTAAGCCGCAACGACGAA-CCAT
**
4796 GTACCACGAAGACACGAAGGG-AAGATTTAAGCCGCAATGGCGAATCCAGTAC
1 GTACCACGAAGACACGAAGGGAAAGATTTAAGCCGCAACAGCGAATCCAGTAC
4848 ATAGCAACAG
Statistics
Matches: 126, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
97 32 0.25
98 19 0.15
99 71 0.56
100 4 0.03
ACGTcount: A:0.38, C:0.21, G:0.26, T:0.15
Consensus pattern (98 bp):
GTACCACGAAGACACGAAGGGAAAGATTTAAGCCGCAACAGCGAATCCAGTACCAAGAAGACATA
AAGGGAAAGATTTAAGCCGCAACGACGAACCAT
Found at i:5015 original size:10 final size:10
Alignment explanation
Indices: 4986--5019 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
4976 GATCAAGCCT
4986 TTGGTTTTAAA
1 TTGG-TTTAAA
4997 TTAGGTTTAAA
1 TT-GGTTTAAA
5008 TTGGTTTAAA
1 TTGGTTTAAA
5018 TT
1 TT
5020 TAAATTTGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.45
11 10 0.45
12 2 0.09
ACGTcount: A:0.29, C:0.00, G:0.18, T:0.53
Consensus pattern (10 bp):
TTGGTTTAAA
Found at i:5023 original size:16 final size:16
Alignment explanation
Indices: 5002--5050 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
4992 TTAAATTAGG
*
5002 TTTAAATTGGTTTAAA
1 TTTAAATTGATTTAAA
*
5018 TTTAAATTTGCTTTAAA
1 TTTAAA-TTGATTTAAA
*
5035 TTTGAATTGATTTAAA
1 TTTAAATTGATTTAAA
5051 ACTTAATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 15 0.52
17 14 0.48
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.51
Consensus pattern (16 bp):
TTTAAATTGATTTAAA
Found at i:5034 original size:17 final size:17
Alignment explanation
Indices: 5002--5042 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
4992 TTAAATTAGG
*
5002 TTTAAA-TTGGTTTAAA
1 TTTAAATTTGCTTTAAA
5018 TTTAAATTTGCTTTAAA
1 TTTAAATTTGCTTTAAA
*
5035 TTTGAATT
1 TTTAAATT
5043 GATTTAAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 6 0.27
17 16 0.73
ACGTcount: A:0.34, C:0.02, G:0.10, T:0.54
Consensus pattern (17 bp):
TTTAAATTTGCTTTAAA
Done.